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sidier (version 3.0.1)
Substitution and Indel Distances to Infer Evolutionary Relationships
Description
Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
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Install
install.packages('sidier')
Monthly Downloads
217
Version
3.0.1
License
GPL-2
Maintainer
AJ MuozPajares
Last Published
February 28th, 2015
Functions in sidier (3.0.1)
Search functions
ex_Coords
example coordinates
spatial.plot
spatial plot of populations
FindHaplo
Find equal haplotypes
HapPerPop
Returns the number of haplotypes per population.
FIFTH
Indel distances following the fifth state rationale
BARRIEL
Indel distances following Barriel method
nt.gap.comb
substitution and indel distance combinations
colour.scheme
internal function for node colour scheme
mutation.network
Haplotype network depiction including mutations
simuEvolution
Simulate sequences evolution
mergeNodes
Merges nodes showing distance values equal to zero
NINA.thr
No Isolated Nodes Allowed network
Example_Spatial.plot_Alignment
example alignment #1 (fasta format)
SIC
Indel distances following the Simple Index Coding method
sidier-package
SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
simplify.network
Network showing modules as nodes
distance.comb
Distance matrices combination
perc.thr
Percolation threshold network
double.plot
Haplotype and population networks including mutations and haplotype frequencies.
pop.dist
Distances among populations
GetHaplo
Get sequences of unique haplotypes
pie.network
Population network depiction including haplotype frequencies
mutationSummary
Summary of observed mutations
zero.thr
Zero distance networks
single.network
Plot a network given a threshold
MCIC
Modified Complex Indel Coding as distance matrix
ex_alignment1
example alignment #1
alignExample
example alignment #1 ('DNAbin' class)